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Chapter

Cover Concepts in Bioinformatics and Genomics

Introduction  

This introductory chapter provides a definition of bioinformatics and a brief exploration of the origins of the term. The chapter then provides examples of the application of bioinformatics in society, academia, and the workplace. Finally, the chapter raises the importance of bioinformatics and its application to genomics.

Chapter

Cover Molecular Diagnostics

Molecular Analysis and Interpreting Molecular Data  

Rifat Hamoudi and Anthony Warford

This chapter focuses on molecular analysis and interpreting molecular data. It looks at the types of data generated from homogenate and intact cell and tissue preparations and considers how these could be analysed through qualitative, semi-quantitative, and quantitative methods. Moreover, the chapter explores bioinformatics as an answer to the interrogation of DNA and RNA target sequences, epigenetic changes, and DNA-protein relationships. It provides an overview of the application of telepathology, and image capture and analysis to achieve diagnosis without requiring microscopy. Finally, the chapter highlights the significance of developing sophisticated bioinformatics algorithms in an effort to correlate data from various sources with clinical pathology data in order to aid the diagnosis of disease and patient management.

Chapter

Cover Introduction to Bioinformatics

Introduction  

This introductory chapter presents the major components of bioinformatics: DNA and protein sequences and structures, genomes and proteomes, databases and information retrieval, the World Wide Web, and computer programming. Before the advent of modern technologies and the internet, biological observations were fundamentally anecdotal and fragmentary. In recent generations, the data have become not only much more quantitative, but also more precise and comprehensive. Biological databases have recently supplemented the archives of nucleic acid sequences, amino acid sequences of proteins, and structures of proteins and protein–nucleic acid complexes. Given the data streams, analysis has become ever more challenging. Not only has bioinformatics developed powerful tools, but its methods are becoming more deeply integrated into the biomedical enterprise.

Chapter

Cover Biophysical Techniques

Computational biology  

Introduction Computational biology is the application of computational methods to all levels of exploration; molecules to ecosystems. This is huge area of research that can be subdivided in various ways. The computer is, of course, also an indispensible tool in every branch of biophysics discussed...

Chapter

Cover Genomics

Rare Diseases: A Genomics Perspective  

This chapter provides an overview of genomics, which is the study of the structure and function of genomes. A genome is the complete set of genetic instructions for an organism. Genomics is a huge area of study that encompasses many different (and sometimes controversial) scientific techniques, which together can help us understand ourselves and the world around us. The chapter then looks at the impact of genomics, starting with how they have changed the way we view some of the most unusual human diseases. Our understanding of rare diseases is rapidly improving, having been accelerated by next-generation sequencing (NGS) technologies and pioneering bioinformatics and statistical techniques. However, new knowledge brings new challenges around the sharing and analysis of data, and new ethical questions around how and when we diagnose and treat rare disease.

Chapter

Cover Exploring proteins: a student’s guide to experimental skills and methods

The important properties of proteins and how to explore them  

This chapter describes the goals and methods employed to separate, identify, and characterize proteins. It begins by considering how to establish the function and structure of a protein and how its activity may be regulated. The chapter then outlines the range of assays used to monitor the biological activity of proteins; such assays underpin protein characterization and purification. The classical approach to studying proteins requires their purification from their native source using bespoke purification procedures for individual proteins. This task has been simplified greatly with the advent of protein expression in recombinant systems. The chapter then looks at how a protein is regulated within the cellular environment and the types of interactions in which it is involved. Typically, this is achieved by monitoring the effects of a number of physical and chemical variables on protein activity. Finally, the chapter discusses the use of bioinformatics in exploring the properties of proteins.

Chapter

Cover Introduction to Glycobiology

Glycomics and analysis of glycan structures  

This chapter focuses on glycomics and provides an analysis of glycan structures. The analysis of glycomes provides a basis for understanding the functions of glycans in cell differentiation and disease. The analysis of glycans on specific glycoproteins and glycolipids is needed to establish their roles as targets for receptor binding. This chapter surveys the most commonly used methods for glycan structure determination and oligosaccharide synthesis, including nuclear magnetic resonance (NMR), glycosidases, and mass spectrometry. Because common sets of glycans are attached to many glycoproteins, the structures that are present can often be identified through routine profiling. Lectins and antibodies can also be used to detect specific sugar structures and are particularly useful for localizing glycans in cells and tissues. Experimental and bioinformatics approaches are being developed to link this information to knowledge about the enzymes that synthesize the glycans and the glycan-binding receptors that recognize them.

Chapter

Cover Concepts in Bioinformatics and Genomics

Protein Structure Prediction  

This chapter concentrates on protein structure prediction programs. It provides strong foundational knowledge of protein structures and the Protein Data Bank. The chapter reviews how secondary and tertiary structures of proteins are experimentally determined and how bioinformatics programs can be used to visualize these structures. However, the structures of many proteins, especially those associated with membranes, are difficult to elucidate through experiments. The chapter then introduces bioinformatics software programs that predict the structures of such proteins. Such predictions can often be verified through biochemical experiments. Finally, the chapter looks at how threading is used to predict tertiary structures and how threading differs from homology modelling.

Chapter

Cover Concepts in Bioinformatics and Genomics

Programming Basics and Applications to Bioinformatics  

This chapter covers the fundamentals of programming using the Python programming language, a popular language for bioinformatics. With a basic understanding of biology, probability, and computer science, the chapter emphasizes that biologists become better users of bioinformatics tools and computer scientists become better developers of bioinformatics tools. The chapter then unravels how data flows through a program through variables. It also demonstrates the data types of Python including integers, floating point numbers, strings, lists, tuples and dictionaries. The chapter then shifts to unfold the creation of useful Python data structures such as a two-dimensional matrix (a list of lists in Python). It also investigates how program execution is controlled by if-tests and loops which use relational and logical operators. Finally, the chapter highlights the use of functions and modules in hierarchical design. It then studies how to develop a Kyte-Doolittle sliding window tool using Python.

Book

Cover Concepts in Bioinformatics and Genomics

Jamil Momand, Alison McCurdy, Silvia Heubach, and Nancy Warter-Perez

Concepts in Bioinformatics and Genomics starts with a review of molecular biology and looks at its relevance to the topic. It then goes on to consider information organization and sequence databases, molecular evolution, substitution matrices, and pairwise sequence alignment. Other topics covered include the basic local alignment sequence tool and multiple sequence alignment, protein structure prediction, phylogenetics, genomics, transcript and protein expression analysis, and basic probability. There are also chapters on advanced probability for bioinformatics applications, programming basics and applications to bioinformatics, and how to develop a basic bioinformatics tool.

Chapter

Cover Concepts in Bioinformatics and Genomics

Review of Molecular Biology  

This chapter offers an overview of molecular biology. It presents the essential biology vocabulary for understanding bioinformatics, then introduces the important molecule, the p53 protein (sometimes referred to as ‘p53’, for short), which plays a significant role in preventing cancer. The chapter also discusses the relationship between genes, transcripts, proteins, and some functions carried out by proteins. It then examines how DNA alterations can lead to protein alterations that affect protein function. The chapter next explains the one-letter code for nucleotides and amino acids. Towards the end, the chapter looks at the term ‘sequence alignment’. It also investigates how the first experiment demonstrating the relationship between a mutation and a disease was carried out.

Chapter

Cover Plants, Genes & Agriculture

Genes, Genomics, and Molecular Biology  

The Basis of Modern Crop Improvement

Kranthi K. Mandadi and T. Erik Mirkov

This chapter begins the consideration of the basic biology that is the foundation of crop-plant improvement by describing genetics, heredity, and molecular biology. The basics of DNA, RNA, and protein synthesis are necessary to an understanding of genes and how/when/where they are expressed; a crucial prerequisite for crop improvement. Gene expression encompasses all the steps from transcription of the DNA to the formation of the final protein. The chapter looks at mutations, which are the basis of polymorphism in the DNA, leading to polymorphism in the individuals of a population. Plant breeders are interested in understanding which polymorphism is associated with which trait. The chapter then highlights the importance of genome sequencing, bioinformatics, and gene editing technologies for plant biologists and breeders.

Chapter

Cover Genetics in Medicine

Laboratory Techniques and the Sequencing Revolution  

This chapter explores laboratory techniques and the sequencing revolution. It examines DNA structure and synthesis as they are applied to laboratory methods. An example is the polymerase chain reaction (PCR). The chapter then highlights how next generation sequencing (NGS) revolutionized molecular diagnostics. It notes the process of analysing DNA sequences to detect pathogenic variants. Moreover, the chapter compares whole genome sequencing and whole exome sequencing, which are both used to diagnose rare diseases. It emphasizes that molecular genetic tests could help diagnose diseases, choose medicine, and screen newborn infants for treatable conditions. The chapter also mentions bioinformatics, which is an emerging clinical science developed alongside the use of whole genome analysis.

Chapter

Cover Concepts in Bioinformatics and Genomics

Basic Probability  

This chapter concentrates on probability, a requisite component of bioinformatics research, with an emphasis on counting methods, dependence, Bayesian inference, and random variables. It develops the basic tools of probability needed to understand bioinformatics applications such as the interpretation of the E-value in the output of a BLAST search, hidden Markov models in algorithms for multiple sequence alignment, and the derivation of the Jukes-Cantor model of evolutionary distance. The chapter opens with a discussion on the basic operations on sets, such as union, intersection, and complement. It discusses the meanings of dependence and independence, then examines how to compute conditional probabilities from the definition or by using Bayes' law. Next, the chapter investigates how to use Bayes' law to compute posterior probabilities from prior probabilities and observed data. It then analyses the probability mass, and the probability density functions in relation to the distribution of a random variable.

Chapter

Cover Introduction to Protein Science

Bioinformatics of protein sequence and structure  

This chapter examines bioinformatics, a new field which is a hybrid of biology and computer science. Biology, especially high-throughput data streams such as DNA sequencing and structural genomics projects, provides its input. Computer science permits the effective use of information-processing equipment to support research based on these data. Databases organize knowledge and make it accessible. Algorithms then allow analysis of the information, thereby producing additional data streams to be incorporated into the repository. The chapter then looks at the concept of sequence alignment, the methods for aligning sequences, and facilities for sequence database searching based on them, notably BLAST (Basic Local Alignment Search Tool) and PSI-BLAST. It also considers the characteristics of pairwise sequence alignment, multiple sequence alignment, and structural alignment.

Chapter

Cover Introduction to Bioinformatics

Alignments and phylogenetic trees  

This chapter examines the concept of sequence alignment, which is the identification of residue-residue correspondences. It is the basic tool of bioinformatics. The chapter presents a comparison of pairwise sequence alignments and multiple sequence alignments. Multiple sequence alignments are much more informative than pairwise sequence alignments, in terms of revealing patterns of conservation. The chapter then looks at the process of constructing and interpreting dot plots, before considering the use of the Hamming distance and Levenshtein distance as measures of dissimilarity of character strings. It also explains the basis of scoring schemes for string alignment, including substitution matrices and gap penalties. Finally, the chapter studies the applications of multiple sequence alignments to database searching, before exploring the contents and significance of phylogenetic trees, and the methods available for deriving them.

Chapter

Cover Introduction to Bioinformatics

Scientific publications and archives: media, content, access, and presentation  

This chapter assesses the trajectory of the development of the scientific literature, and how it has affected the practice of science. Classically, scientists presented their major results as full-length books. Today, in addition to journals, formats of scientific publication include presentations at meetings; books, or chapters contributed to books; material on the web, including blogs; films; radio or television programmes; podcasts; and social media such as Twitter. Indeed, the World Wide Web provides an alternative to paper as a mechanism of distribution of the scientific literature. The chapter then looks at the differences in accessibility and convenience between paper and computer access to scientific journals, as well as the differences between traditional and digital libraries. It also considers the explosion of scientific information; the principles of markup languages; the different types of computer languages; and the power and limitations of natural language processing by computer, and its applications in bioinformatics.

Chapter

Cover Introduction to Bioinformatics

Structural bioinformatics and drug discovery  

This chapter focuses on structural bioinformatics and drug discovery. Understanding protein structures in detail is essential for determining their functions and mechanisms of action, and for clinical and pharmacological applications. The chapter begins by looking at the concept of protein folding: the process by which the one-dimensional amino acid sequence encoded by a gene takes up a definite and biologically active three-dimensional conformation. It then considers the hydrophobic effect and its implications for the structures and energetics of folded proteins. The chapter also outlines the classification of protein folding patterns, as presented by the Structural Classification of Proteins (SCOP) database and website. Finally, the chapter presents some basic approaches to the prediction of protein structure from amino acid sequence, and the Critical Assessment of Structure Prediction (CASP) programs.